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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ), 'gf_id' => 'HOM05D001274', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001274' ), 'data_identifier' => 'HOM05D001274', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001274', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10070' => 'bna', 'A02p04740' => 'bna', 'A03p08650' => 'bna', 'A03p51000' => 'bna', 'A04p09800' => 'bna', 'A05p16480' => 'bna', 'A07p10550' => 'bna', 'A08p09820' => 'bna', 'A08p13460' => 'bna', 'A09p36820' => 'bna', 'A10p21390' => 'bna', 'Aa31LG11G11490' => 'aar', 'Aa31LG5G14430' => 'aar', 'Aa31LG6G6050' => 'aar', 'Aa31LG6G780' => 'aar', 'Aa31sc878G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.604' => 'aag', 'Actinidia02875' => 'ach', 'Actinidia11367' => 'ach', 'Actinidia16755' => 'ach', 'Actinidia17300' => 'ach', 'Actinidia19479' => 'ach', 'Actinidia20834' => 'ach', 'Actinidia22078' => 'ach', 'Actinidia38610' => 'ach', 'Actinidia39924' => 'ach', 'Ah.04g155340' => 'amhyb', 'Ah.09g233000' => 'amhyb', 'Ah.13g066390' => 'amhyb', 'Ah.14g086790' => 'amhyb', 'AL1G43400' => 'aly', 'AL1G43440' => 'aly', 'AL6G29310' => 'aly', 'AL7G36400' => 'aly', 'AL7G44470' => 'aly', 'Aqoxy1G01875' => 'aox', 'Aqoxy2G00517' => 'aox', 'Aqoxy2G03728' => 'aox', 'Aqoxy6G01545' => 'aox', 'arahy.Tifrunner.gnm1.ann1.15JPRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VS1VF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3QMRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DGK6GV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DIJ55H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9ZGWL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L0AG4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY5T03' => 'arhy', 'AT1G29550' => 'ath', 'AT1G29590' => 'ath', 'AT4G18040' => 'ath', 'AT5G18110' => 'ath', 'AT5G35620' => 'ath', 'ATR0736G056' => 'atr', 'ATR0737G051' => 'atr', 'ATR0763G096' => 'atr', 'Atru.chr10.1456' => 'acertr', 'Atru.chr4.1936' => 'acertr', 'AUR62016176' => 'cqu', 'AUR62025064' => 'cqu', 'AUR62027533' => 'cqu', 'AUR62032037' => 'cqu', 'AUR62032543' => 'cqu', 'AUR62032714' => 'cqu', 'AUR62035094' => 'cqu', 'AUR62035821' => 'cqu', 'BcaB01g05175' => 'bca', 'BcaB01g06397' => 'bca', 'BcaB02g08051' => 'bca', 'BcaB03g13877' => 'bca', 'BcaB04g18025' => 'bca', 'BcaB04g18453' => 'bca', 'BcaB04g18614' => 'bca', 'BcaB05g23303' => 'bca', 'BcaB06g26951' => 'bca', 'BcaB07g32546' => 'bca', 'BcaB08g34853' => 'bca', 'BcaB08g36705' => 'bca', 'BcaC02g09484' => 'bca', 'BcaC03g13577' => 'bca', 'BcaC04g18723' => 'bca', 'BcaC06g33602' => 'bca', 'BcaC06g33603' => 'bca', 'BcaC06g35440' => 'bca', 'BcaC07g37654' => 'bca', 'BcaC07g38111' => 'bca', 'BcaC08g44313' => 'bca', 'BcaC09g51556' => 'bca', 'BcaNung00034' => 'bca', 'BolC1t01164H' => 'bol', 'BolC2t06879H' => 'bol', 'BolC3t13495H' => 'bol', 'BolC4t25909H' => 'bol', 'BolC5t31557H' => 'bol', 'BolC6t36933H' => 'bol', 'BolC7t42108H' => 'bol', 'BolC7t45446H' => 'bol', 'BolC7t45447H' => 'bol', 'BolC8t48029H' => 'bol', 'BolC8t48534H' => 'bol', 'BolC9t58731H' => 'bol', 'BraA01t00953Z' => 'bra', 'BraA02t05433Z' => 'bra', 'BraA03t10188Z' => 'bra', 'BraA03t14185Z' => 'bra', 'BraA04t16641Z' => 'bra', 'BraA05t20553Z' => 'bra', 'BraA07t28852Z' => 'bra', 'BraA08t32975Z' => 'bra', 'BraA08t33323Z' => 'bra', 'BraA09t39200Z' => 'bra', 'BraA10t44202Z' => 'bra', 'C01p11890' => 'bna', 'C02p09700' => 'bna', 'C03p10090' => 'bna', 'C04p43290' => 'bna', 'C05p28380' => 'bna', 'C06p17380' => 'bna', 'C07p16160' => 'bna', 'C07p49400' => 'bna', 'C07p49410' => 'bna', 'C09p58870' => 'bna', 'CAN.G128.61' => 'can', 'CAN.G187.12' => 'can', 'CAN.G220.84' => 'can', 'CAN.G638.20' => 'can', 'CANSAT35G0883' => 'cansat', 'CANSAT56G4513' => 'cansat', 'CARHR028940' => 'chi', 'CARHR194960' => 'chi', 'CARHR217790' => 'chi', 'CARHR224810' => 'chi', 'Carub.0001s2779' => 'cru', 'Carub.0001s2781' => 'cru', 'Carub.0006s1640' => 'cru', 'Carub.0007s2329' => 'cru', 'Carub.0007s3136' => 'cru', 'Ca_00500_v3' => 'car', 'Ca_04482_v3' => 'car', 'Ca_11921_v3' => 'car', 'Ca_22219_v3' => 'car', 'CBR_g29302' => 'cbr', 'CBR_g41160' => 'cbr', 'CBR_g48778' => 'cbr', 'Cc03_g06040' => 'ccan', 'Cc06_g23090' => 'ccan', 'Cc09_g09960' => 'ccan', 'CDE01G0486' => 'cde', 'CDE01G0636' => 'cde', 'CDE02G0456' => 'cde', 'CDE02G0626' => 'cde', 'CDE02G2084' => 'cde', 'CDE02G4458' => 'cde', 'CDE05G0663' => 'cde', 'CDE12G0664' => 'cde', 'Cfa001055' => 'cfa', 'Cfa014774' => 'cfa', 'Cfa017656' => 'cfa', 'Cfa026730' => 'cfa', 'Ciclev10005943m.g' => 'ccl', 'Ciclev10016586m.g' => 'ccl', 'Ciclev10022151m.g' => 'ccl', 'CiPaw.01G179100' => 'cil', 'CiPaw.02G107800' => 'cil', 'CiPaw.09G131800' => 'cil', 'CiPaw.10G097900' => 'cil', 'CiPaw.10G127300' => 'cil', 'ClCG03G007240' => 'cla', 'ClCG06G007220' => 'cla', 'ClCG10G013430' => 'cla', 'ClCG10G013440' => 'cla', 'COL.COLO4_07052' => 'col', 'COL.COLO4_22812' => 'col', 'COL.COLO4_36087' => 'col', 'Cpa.g.sc17.108' => 'cpa', 'Cpa.g.sc44.11' => 'cpa', 'Cpa.g.sc51.133' => 'cpa', 'Cre03.g199900' => 'cre', 'CsaV3_1G032830' => 'csa', 'CsaV3_2G012490' => 'csa', 'CsaV3_3G043200' => 'csa', 'CSS0003215' => 'camsi', 'CSS0008632' => 'camsi', 'CSS0031786' => 'camsi', 'CSS0039904' => 'camsi', 'DCAR_002303' => 'dca', 'DCAR_017050' => 'dca', 'DCAR_020901' => 'dca', 'DCAR_027340' => 'dca', 'Dinv14572' => 'din', 'Dinv27098' => 'din', 'Dinv29812' => 'din', 'Dinv32306' => 'din', 'Duzib106G1441' => 'dzi', 'Duzib151G0393' => 'dzi', 'Duzib192G0697' => 'dzi', 'Duzib212G0057' => 'dzi', 'Duzib235G0053' => 'dzi', 'ECA234G1073' => 'eca', 'ECA236G2961' => 'eca', 'EL10Ac3g04952' => 'bvu', 'EL10Ac3g06830' => 'bvu', 'EL10Ac8g19813' => 'bvu', 'Eucgr.A02106' => 'egr', 'Eucgr.D00351' => 'egr', 'Eucgr.E02874' => 'egr', 'Eucgr.H02962' => 'egr', 'FAN11G2823' => 'fan', 'FAN12G3327' => 'fan', 'FAN14G2553' => 'fan', 'FAN16G2101' => 'fan', 'FAN17G0079' => 'fan', 'FAN19G3098' => 'fan', 'FAN21G0651' => 'fan', 'FAN22G2221' => 'fan', 'FAN23G2073' => 'fan', 'FAN25G3846' => 'fan', 'FAN26G2031' => 'fan', 'FAN28G1771' => 'fan', 'FAN28G2225' => 'fan', 'FvH4_1g28260' => 'fve', 'FvH4_2g26760' => 'fve', 'FvH4_3g06500' => 'fve', 'FvH4_4g04440' => 'fve', 'FvH4_6g40690' => 'fve', 'Glyma.02G072700' => 'gma', 'Glyma.10G136100' => 'gma', 'Glyma.13G222400' => 'gma', 'Glyma.15G089800' => 'gma', 'Glyma.16G153800' => 'gma', 'Glyma.20G085800' => 'gma', 'Gohir.A02G042300' => 'ghi', 'Gohir.A05G151800' => 'ghi', 'Gohir.A06G198300' => 'ghi', 'Gohir.A10G108600' => 'ghi', 'Gohir.A13G099500' => 'ghi', 'Gohir.D02G047900' => 'ghi', 'Gohir.D05G154200' => 'ghi', 'Gohir.D06G205700' => 'ghi', 'Gohir.D10G159200' => 'ghi', 'Gohir.D13G102900' => 'ghi', 'Gorai.005G053200' => 'gra', 'Gorai.009G158500' => 'gra', 'Gorai.010G240000' => 'gra', 'Gorai.011G178800' => 'gra', 'Gorai.013G115200' => 'gra', 'GSVIVG01021323001' => 'vvi', 'GSVIVG01027903001' => 'vvi', 'GSVIVG01033412001' => 'vvi', 'HanXRQChr02g0054581' => 'han', 'HanXRQChr04g0116341' => 'han', 'HanXRQChr13g0397851' => 'han', 'HanXRQChr14g0434841' => 'han', 'HanXRQChr16g0526071' => 'han', 'HanXRQChr17g0564901' => 'han', 'Haze_05461' => 'cav', 'Haze_11448' => 'cav', 'Haze_20495' => 'cav', 'Haze_27629' => 'cav', 'Hma1.2p1_0012F.1_g007700' => 'hma', 'Hma1.2p1_0152F.1_g067590' => 'hma', 'Hma1.2p1_2113F.1_g314250' => 'hma', 'HPP92_000197' => 'vpl', 'HPP92_000232' => 'vpl', 'HPP92_021223' => 'vpl', 'HPP92_021227' => 'vpl', 'HPP92_021228' => 'vpl', 'HPP92_021386' => 'vpl', 'HPP92_022495' => 'vpl', 'HPP92_022500' => 'vpl', 'HPP92_022501' => 'vpl', 'Hund03082' => 'sun', 'Hund19230' => 'sun', 'Hund21468' => 'sun', 'Hund27523' => 'sun', 'Hund27530' => 'sun', 'Lalb_Chr01g0020291' => 'lal', 'Lalb_Chr02g0157171' => 'lal', 'Lalb_Chr03g0036991' => 'lal', 'Lalb_Chr06g0174011' => 'lal', 'Lalb_Chr15g0086561' => 'lal', 'Lalb_Chr18g0055081' => 'lal', 'Lj1A1136T60' => 'lonja', 'Lj2A312G57' => 'lonja', 'Lj2g0024720' => 'lja', 'Lj6A622T57' => 'lonja', 'Lj6g0017296' => 'lja', 'Lj6g0019784' => 'lja', 'Lsat_1_v5_gn_2_40760' => 'lsa', 'Lsat_1_v5_gn_4_27581' => 'lsa', 'Lsat_1_v5_gn_6_37480' => 'lsa', 'Lsat_1_v5_gn_6_68620' => 'lsa', 'Lsat_1_v5_gn_7_26440' => 'lsa', 'Manes.03G160000' => 'mes', 'Manes.08G145200' => 'mes', 'Manes.09G140300' => 'mes', 'Manes.15G044900' => 'mes', 'Manes.17G063100' => 'mes', 'Mapoly0005s0006' => 'mpo', 'Mapoly0034s0012' => 'mpo', 'MBI01_g25636_MAGBIO' => 'mbi', 'MBI10_g30721_MAGBIO' => 'mbi', 'MBI15_g07477_MAGBIO' => 'mbi', 'MCO01G204' => 'mco', 'MD05G1292800' => 'mdo', 'MD10G1268600' => 'mdo', 'MD10G1268700' => 'mdo', 'MD12G1004900' => 'mdo', 'MD13G1219900' => 'mdo', 'MD14G1003400' => 'mdo', 'MD16G1225300' => 'mdo', 'Medtr1g045130' => 'mtr', 'Medtr2g018260' => 'mtr', 'Medtr6g029230' => 'mtr', 'MELO3C002698.2' => 'cme', 'MELO3C023037.2' => 'cme', 'MELO3C026612.2' => 'cme', 'Migut.G00484' => 'egut', 'Migut.J01883' => 'egut', 'Migut.M00968' => 'egut', 'Migut.M01057' => 'egut', 'Migut.N00295' => 'egut', 'MSTRG.14751' => 'ama', 'MSTRG.19930' => 'ama', 'MSTRG.21924' => 'ama', 'MSTRG.7453' => 'ama', 'Nitab4.5_0000165g0130' => 'nta', 'Nitab4.5_0000394g0110' => 'nta', 'Nitab4.5_0000658g0050' => 'nta', 'Nitab4.5_0000982g0040' => 'nta', 'Nitab4.5_0000982g0070' => 'nta', 'Nitab4.5_0000982g0080' => 'nta', 'Nitab4.5_0001051g0140' => 'nta', 'Nitab4.5_0001079g0170' => 'nta', 'Nitab4.5_0002709g0010' => 'nta', 'Nitab4.5_0002814g0120' => 'nta', 'Nitab4.5_0003475g0030' => 'nta', 'Nitab4.5_0008487g0040' => 'nta', 'Nitab4.5_0013012g0010' => 'nta', 'Nn1g02930' => 'nnu', 'Nn2g12052' => 'nnu', 'Nn3g19757' => 'nnu', 'Nn3g20951' => 'nnu', 'Nn6g34384' => 'nnu', 'Nn7g35874' => 'nnu', 'Oeu002291.1' => 'oeu', 'Oeu040945.1' => 'oeu', 'Oeu046740.1' => 'oeu', 'Oeu046831.1' => 'oeu', 'Os01g0970400' => 'osa', 'Os03g0262400' => 'osa', 'Os10g0467600' => 'osa', 'Peaxi162Scf00033g00293' => 'pax', 'Peaxi162Scf00121g10119' => 'pax', 'Peaxi162Scf00249g00716' => 'pax', 'Peaxi162Scf00463g00121' => 'pax', 'Peaxi162Scf00899g00039' => 'pax', 'PGR004G1741' => 'pgr', 'PGR042G0844' => 'pgr', 'PGR042G3340' => 'pgr', 'PGSC0003DMG400013421' => 'stu', 'PGSC0003DMG400023664' => 'stu', 'PGSC0003DMG401017153' => 'stu', 'Phvul.004G080900' => 'pvu', 'Phvul.006G168400' => 'pvu', 'Phvul.007G270900' => 'pvu', 'Potri.008G171100' => 'ptr', 'Potri.010G066700' => 'ptr', 'Potri.011G077200' => 'ptr', 'Potri.013G057000' => 'ptr', 'Pp3c11_1600' => 'ppa', 'Pp3c1_5840' => 'ppa', 'Pp3c1_5850' => 'ppa', 'Pp3c26_10900' => 'ppa', 'Pp3c2_32310' => 'ppa', 'Pp3c4_24310' => 'ppa', 'PRCOL_00001042' => 'pco', 'PRCOL_00004626' => 'pco', 'Prupe.1G046600' => 'ppe', 'Prupe.4G072600' => 'ppe', 'Prupe.7G005900' => 'ppe', 'Psat1g095480' => 'psa', 'Psat1g192480' => 'psa', 'Psat6g106240' => 'psa', 'PSO339G4596' => 'pso', 'PSO384G2601' => 'pso', 'PSO541G3441' => 'pso', 'PSO541G4789' => 'pso', 'PSO674G0106' => 'pso', 'PSO675G1770' => 'pso', 'PSO675G7291' => 'pso', 'PSO832G0645' => 'pso', 'QL05p052877' => 'qlo', 'QL06p020774' => 'qlo', 'QL07p018522' => 'qlo', 'RcHm_v2.0_Chr1g0351341' => 'rch', 'RcHm_v2.0_Chr3g0496901' => 'rch', 'RcHm_v2.0_Chr4g0395001' => 'rch', 'RcHm_v2.0_Chr5g0012781' => 'rch', 'Rhsim02G0151800' => 'rsi', 'Rhsim03G0001600' => 'rsi', 'Rhsim04G0173300' => 'rsi', 'Sabra10G0040700' => 'sbr', 'Sabra11G0064200' => 'sbr', 'Sabra13G0050700' => 'sbr', 'Sabra16G0233700' => 'sbr', 'SalBow3G1986' => 'sbo', 'SalBow6G3035' => 'sbo', 'SalBow7G2139' => 'sbo', 'SalBow7G2594' => 'sbo', 'SalBow7G4750' => 'sbo', 'Sc17g0005420' => 'sci', 'Sc19g0006370' => 'sci', 'Sc24g0001910' => 'sci', 'Sc25g0003590' => 'sci', 'Sed0005286' => 'sed', 'Sed0012110' => 'sed', 'Sed0014550' => 'sed', 'Sed0026645' => 'sed', 'Sed0027973' => 'sed', 'Sed0028221' => 'sed', 'SEGI_03804' => 'sgi', 'SEGI_09500' => 'sgi', 'SEGI_32524' => 'sgi', 'SEGI_40951' => 'sgi', 'SGA_v2.0_scaffold16G07731' => 'sas', 'SGA_v2.0_scaffold1G00122' => 'sas', 'SGA_v2.0_scaffold281G46878' => 'sas', 'SGA_v2.0_scaffold31G12642' => 'sas', 'SGA_v2.0_scaffold31G12672' => 'sas', 'SGA_v2.0_scaffold43G16200' => 'sas', 'SMO010G0020' => 'smo', 'SMO201G0086' => 'smo', 'SMO228G0042' => 'smo', 'SMO268G0047' => 'smo', 'SMO339G0011' => 'smo', 'Solyc02g021550.3' => 'sly', 'Solyc03g005870.4' => 'sly', 'Solyc09g090580.3' => 'sly', 'Solyc10g080660.3' => 'sly', 'Sopen02g006080' => 'spe', 'Sopen03g001880' => 'spe', 'Sopen09g033520' => 'spe', 'Sopen10g031200' => 'spe', 'Sp1g25490' => 'spa', 'Sp3g02820' => 'spa', 'Sp6g26200' => 'spa', 'Sp7g06640' => 'spa', 'TAR198G0001' => 'tar', 'TAR362G0364' => 'tar', 'TAR365G1024' => 'tar', 'TAR626G1313' => 'tar', 'TAR633G0747' => 'tar', 'TAR633G1535' => 'tar', 'THA.LOC104802872' => 'tha', 'THA.LOC104806109' => 'tha', 'THA.LOC104808876' => 'tha', 'THA.LOC104814271' => 'tha', 'THA.LOC104826604' => 'tha', 'THA.LOC104827739' => 'tha', 'Thecc.04G262400' => 'tca', 'Thecc.05G249500' => 'tca', 'Thecc.06G159400' => 'tca', 'Thhalv10004946m.g' => 'esa', 'Thhalv10008588m.g' => 'esa', 'Thhalv10014598m.g' => 'esa', 'Thhalv10019733m.g' => 'esa', 'Thhalv10021831m.g' => 'esa', 'Thhalv10026131m.g' => 'esa', 'TPR.G20634' => 'tpr', 'TPR.G23966' => 'tpr', 'TPR.G39885' => 'tpr', 'TPR.G9147' => 'tpr', 'TWI09G0907' => 'twi', 'TWI09G1080' => 'twi', 'TWI09G1492' => 'twi', 'TWI32G0307' => 'twi', 'TWI34G1396' => 'twi', 'TWI53G0378' => 'twi', 'TWI73G1025' => 'twi', 'unitig_52.g17407' => 'ugi', 'vmacro03986' => 'vma', 'vmacro08546' => 'vma', 'vmacro09133' => 'vma', 'vmacro12562' => 'vma', 'VMungo0464G0301' => 'vmu', 'VMungo0540G0578' => 'vmu', 'VMungo0720G3153' => 'vmu', 'Zm00001eb011490' => 'zma', 'Zm00001eb046430' => 'zma', 'Zm00001eb137550' => 'zma', 'Zm00001eb139930' => 'zma', 'Zm00001eb222060' => 'zma' ) $gf_id = 'HOM05D001274' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001274' ) $data_identifier = 'HOM05D001274' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 23, 'bol' => (int) 12, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb222060' $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